|
| Status |
Public on Jun 09, 2023 |
| Title |
Menin-ChIP, 1014 sgKdm6a, VTP, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse small cell lung cancer (SCLC) tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: mouse small cell lung cancer (SCLC) tumor
cell line: 1014 sgKdm6a
cell type: mouse small cell lung cancer tumor-derived cells
strain: pure congenic Lox-stop-lox (LSL) Cas9 BL6J mice
chip antibody: Menin (Bethyl, A300-105A)
treatment: VTP50469
|
| Treatment protocol |
Cells were treated with VTP-50469 (500 nM) or DMSO for 5 days for each replicate
|
| Growth protocol |
Cells were counted and plated at 0.1x106 per mL in 100 mLs (10 X 107 cells total) for each condition.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified with AMPure XP beads (Beckman Coulter). DNA fragments were quantified by TapeStation 4200 (Agilent) using HSD1000 Tape and Reagent (Agilent) and Qubit (ThermoFisher).
1-10 ng of DNA was used in preparation of Illumina compatible libraries using SMARTer ThruPLEX DNA-Seq Kit (Takara) followed by sequencing using NextSeq550 (Illumina) to obtain 20-30 million 37bp, paired-end reads. Reads (paired-end 37mers) were aligned to the mouse (Gencode M24/mm10) genome using STAR (v2.7.5a; params –alignIntronMax 1 –alignEndsType EndToEnd – alignMatesGapMax 2000 for ChIP-seq analysis), sorted, and duplicates were marked/removed with picard pipeline tools (v2.9.4). Final “deduped” .BAM files were indexed using SAMtools (v1.95)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
ChIP-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75)
Assembly: mm10
Supplementary files format and content: tdf
|
| |
|
| Submission date |
Mar 28, 2023 |
| Last update date |
Jun 09, 2023 |
| Contact name |
Leslie Duplaquet |
| E-mail(s) |
leslie_duplaquet@dfci.harvard.edu
|
| Organization name |
DFCI
|
| Department |
Medical Oncology
|
| Lab |
Oser Lab
|
| Street address |
360 Longwood Ave
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE228345 |
Small Cell Lung Cancer Subtype Plasticity is Regulated by KDM6A/UTX [ChIP-Seq] |
| GSE228347 |
KDM6A Epigenetically Regulates Subtype Plasticity in Small Cell Lung Cancer |
|
| Relations |
| BioSample |
SAMN33944407 |
| SRA |
SRX19790758 |
